Contacts of the helix formed by residues 487 - 498 (chain D) in PDB entry 4BGG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 487 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404D ILE* 3.9 4.9 - - - -
485D ARG 5.0 2.7 - - - +
486D LEU* 1.3 79.3 - - - +
488D ALA* 1.3 64.3 + - - +
489D LEU* 3.5 7.9 + - - +
490D ARG* 3.1 25.0 + - - +
491D ILE* 3.1 24.9 + - - +
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Residues in contact with ALA 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D ALA* 4.5 4.8 - - - +
316D LEU* 4.2 8.7 - - + -
317D ALA* 3.7 32.2 - - - +
320D HIS* 3.7 24.4 + - + +
404D ILE* 3.5 16.6 - - + +
487D THR* 1.3 73.8 - - - +
489D LEU* 1.3 63.0 - - - +
491D ILE* 3.3 7.7 + - - +
492D LYS* 3.1 22.9 + - - +
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Residues in contact with LEU 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ALA* 4.2 11.3 - - + +
487D THR* 3.2 8.7 + - - +
488D ALA* 1.3 79.6 - - - +
490D ARG* 1.3 56.3 + - - +
492D LYS* 3.2 23.7 + - + +
493D LYS* 3.0 59.3 + - + +
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Residues in contact with ARG 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486D LEU* 4.6 15.9 - - + -
487D THR* 3.1 26.2 + - + +
489D LEU* 1.3 73.9 - - - +
491D ILE* 1.3 66.7 + - - +
493D LYS* 3.3 9.9 + - - +
494D THR* 2.9 30.5 + - - +
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Residues in contact with ILE 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D ALA* 4.1 4.3 - - + -
316D LEU* 6.1 0.4 - - + -
404D ILE* 4.1 17.0 - - + -
407D PHE* 3.5 44.2 - - + -
411D LEU* 5.4 0.2 - - + -
473D LEU* 4.2 17.2 - - + +
477D CYS* 3.8 17.3 - - - -
486D LEU* 3.8 22.9 - - + -
487D THR 3.1 16.3 + - - +
488D ALA* 3.6 8.3 - - - +
490D ARG* 1.3 75.5 - - - +
492D LYS* 1.3 57.4 + - - +
494D THR* 3.4 1.7 + - - -
495D LEU* 2.9 44.5 + - + +
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Residues in contact with LYS 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D HIS* 5.7 2.8 + - - -
310D LEU* 3.9 11.3 - - + +
313D ALA* 4.2 14.6 - - + +
314D SER* 3.5 42.8 + - - +
317D ALA* 4.5 11.9 - - + +
488D ALA 3.1 13.4 + - - +
489D LEU* 3.4 21.6 - - + +
491D ILE* 1.3 78.9 - - - +
493D LYS* 1.3 57.8 + - + +
495D LEU* 3.4 1.7 + - - +
496D THR* 2.8 40.0 + - - +
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Residues in contact with LYS 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489D LEU* 3.0 51.2 + - + +
490D ARG* 3.3 8.3 + - - +
492D LYS* 1.3 79.0 - - + +
494D THR* 1.3 62.6 + - - +
496D THR* 3.3 8.0 + - - -
497D LYS* 3.0 22.9 + - - +
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Residues in contact with THR 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D SER* 5.7 4.9 - - - +
473D LEU* 4.2 29.0 - - + +
486D LEU* 5.6 1.2 - - - +
490D ARG* 2.9 18.9 + - - +
491D ILE 3.8 3.8 - - - -
493D LYS* 1.3 76.7 - - - +
495D LEU* 1.3 61.7 + - - +
497D LYS* 3.3 16.3 + - + +
498D ILE* 3.6 17.4 + - + +
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Residues in contact with LEU 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D LEU* 4.4 12.8 - - + +
309D VAL* 3.8 40.6 - - + +
310D LEU* 3.9 18.8 - - + +
313D ALA* 4.0 7.6 - - + -
407D PHE* 4.6 3.1 - - + -
411D LEU* 5.5 0.9 - - + -
470D LEU* 3.5 32.5 - - + -
473D LEU* 3.6 15.7 - - + -
491D ILE* 2.9 37.3 + - + +
492D LYS 3.9 3.1 - - - +
494D THR* 1.3 71.7 - - - +
496D THR* 1.3 66.3 + - - +
498D ILE* 3.2 24.9 + - + +
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Residues in contact with THR 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D LEU* 3.8 21.7 - - + +
492D LYS* 2.8 30.1 + - - +
493D LYS* 3.3 8.6 + - - -
495D LEU* 1.3 77.7 - - - +
497D LYS* 1.3 62.3 + - - +
498D ILE 3.0 10.0 + - - -
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Residues in contact with LYS 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D LYS 3.0 12.4 + - - +
494D THR* 3.3 12.9 + - + +
496D THR* 1.3 75.0 - - - +
498D ILE* 1.3 59.9 + - + +
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Residues in contact with ILE 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D LEU* 3.8 40.4 - - + +
466D THR* 4.6 13.9 - - + +
469D SER* 3.6 33.9 - - - +
470D LEU* 5.2 1.8 - - + -
473D LEU* 5.9 0.4 - - + -
494D THR* 3.6 17.9 + - + +
495D LEU* 3.2 22.8 + - + +
496D THR 3.0 11.7 + - - -
497D LYS* 1.3 82.1 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il